Chapter 12 Pathways to Biomolecules

BiomoleculesBiomoleculesBiomolecules Are Compounds of Carbon with a Variety of Functional Groups- more than half the dry weight of cells. - fats and oils, carbohydrates, proteins and nucleic acids.They have an essential role in the supply of energy to the body, the growth and repair of organs and tissue, the movement of muscles, the activity of nervous and hormonal systems and the elimination of waste.Many biomolecules are polymers.

Versatility of carbon bonding. Carbon can form covalentsingle, double, and triple bonds (in red), particularly with other carbon atoms. Triple bonds are rare in biomolecules.

Geometry of carbon bonding. (a) Carbon atoms have a characteristic tetrahedral arrangement of their four single bonds. (b) Carboncarbon single bonds have freedom of rotation, as shown for the compound ethane (CH3OCH3). (c) Double bonds are shorter and do not allow free rotation. The two doubly bonded carbons andthe atoms designated A, B, X, and Y all lie in the same rigid plane.

Cells Contain a Universal Set of Small Molecules- Dissolved in the aqueous phase (cytosol) of all cells is a collection of 100 to 200 different small organic molecules(Mr ~100 to ~500),

- collection of molecules includes thecommon amino acids, nucleotides, sugars and their phosphorylated derivatives, and a number of mono-, di-, and tricarboxylic acids.

- The molecules are polar or charged, water soluble, and present in micromolar tomillimolar concentrations.

- There are other small biomolecules, specific to certain types of cells or organisms. For example, vascular plants contain, in addition to the universal set, small molecules called secondary metabolites, which play a role specific to plant life. - These metabolites include compounds that give plants their characteristic scents, and compounds such as morphine, quinine, nicotine, and caffeine that are valued for their physiological effects on humans but used for other purposes by plants.

- The entire collection of small molecules in a given cell has been called that cells metabolome, in parallel with the term genome

Macromolecules Are the Major Constituents of CellsSynthesis of macromolecules isa major energy-consuming activity of cells. Macromolecules themselves may be further assembled into supramolecular complexes, forming functional units such as ribosomes. Proteins, long polymers of amino acids,- constitute the largest fraction (besides water) of cells. -Some proteins have catalytic activity and function as enzymes;- others serve as structural elements, signal receptors, or transporters that carry specific substances into or out of cells.Proteins are perhaps the most versatile of all biomolecules. The nucleic acids, DNA and RNA, are polymers of nucleotides. They store and transmit genetic information, and some RNA molecules have structural and catalytic roles in supramolecular complexes. The polysaccharides, polymers of simple sugars glucose, have two major functions: as energy-yielding fuel stores and as extracellular structural elements with specific binding sites for particular proteins. Shorter polymers of sugars (oligosaccharides) attached to proteins or lipids at the cell surface serve as specific cellular signals. The lipids, greasy or oily hydrocarbon derivatives, serve as structural components of membranes, energy-rich fuel stores, pigments, and intracellular signals. In proteins, nucleotides, polysaccharides, and lipids, the number of monomeric subunits is very large: molecular weights in the range of 5,000 to more than 1 million for proteins, up to several billion for nucleic acids, and in the millions for polysaccharides such as starch. Individual lipid molecules are much smaller (Mr 750 to 1,500) and are not classified as macromolecules. However, large numbers of lipid molecules can associate noncovalently into very large structures. Cellular membranes are built of enormous noncovalent aggregates of lipid and protein molecules.FatsHumans can make their own fat internally.Though this is not usually necessary as fat is readily available in the food we eat.Fat is a name used to describe a large number of organic compounds belonging to an even larger class of biological molecules called lipids.Fats and oils are the best known types of lipids.Fats contOil in food have very different structures and properties from hydrocarbon oils.Compounds such as waxes and steroids (which include cholesterol) are also lipids.Lipids are based mainly on carbon and hydrogen.They also contain small amounts of oxygen and sometimes some other elements.Most lipids are non-polar and insoluble in water. Fats and OilsHave very similar chemical structures.They are simply distinguished on the basis of their physical states at normal temperatures:Fats are solidsOils are liquidsMost fats and oils are formed by a condensation reaction between a single molecule of glycerol and three molecules of fatty acids.Fatty acids contain a carboxyl functional group which reacts with the hydroxyl groups in the glycerol.The COO- groups in fat are ester linkages.Three molecules of water are also produced in this reaction.Fats and oils formed from this process are called triglycerides.Most fats have two or three different fatty acids attached to the glycerol molecule.Triglycerides are large, non-polar molecules and therefore are insoluble in aqueous.

Types of FatsFats are distinguishable on the basis of the fatty acids from which they are made:Saturated fats are made from fatty acids, such as palmitic acid, that contain only single carbon-carbon bonds. Saturated fats are generally unreactive and occur as waxy solids at room temperature.Monounsaturated fats are made from fatty acids, such as oleic acid, that contain one carbon-carbon double bond.Polyunsaturated fats are made from fatty acids, such as linoleic acid, that contain more than one carbon-carbon double bond. Polyunsaturated fats have lower melting temperatures than saturated fats and often occur at liquids, oils, are room temperature. They are more reactive than saturated fats.Types of Fats contThe different physical states of saturated and polyunsaturated fats are thought to arise because molecules of saturated fats can pack more closely together, resulting in stronger dispersion forces between the molecules.The arrangement of the carbon chain sections at the double bond sites of polyunsaturated fats do not permit close packing.Consequently saturated fats have higher melting points than unsaturated fats. What happens to fat in the body?Chemical digestion of fat does not start until it reaches the small intestine.There it is mixed with bile, from the gall bladder.Bile contains surfactants that convert the fats into an emulsion of smaller fat globules.This increases the surface area, meaning it is able to react more rapidly.Secretions from the pancreas and the walls of the small intestine contain enzymes that catalyse the hydrolysis of fat into fatty acids and glycerol; reversing the condensation reaction from which fat was made.Enzymes in the small intestine operate best under alkaline conditions.Once the fatty acids and glycerol have been absorbed into the body, they are reassembled into triglycerides via condensation reactions. Condensation and PolymerisationThe monomers used to make polymers by a condensation polymerisation reaction have a pair of functional groups that are able to react together, producing a new functional groups that links monomers and also produces a small molecule such as water.Synthetic polymers such as nylon and polyester are formed in this way, are proteins, DNA, cellulose and starch.CarbohydratesThe main structural component of all plants is a polymer called cellulose.Cellulose belongs to a class of compounds called carbohydrates.Green plants in the presence of sunlight, convert carbon dioxide and water into a number of substances including the carbohydrate glucose.CHOs are a source of energy in our diets.CHOs are made from the element C, H and O and usually have the formula Cx(H2O)y, where x and y are whole numbers.Carbohydrates contCHOs range in size from small molecules, with Mrs of between 100 and 200 to very large polymers with Mr greater than 1 million.MonosaccharidesAre the smallest CHOs.The are white crystalline solids that highly soluble in water. Most monosaccharides have a sweet taste.Monsaccharides together with another group of CHOs called disaccharides are often called sugars.The most abundant monosaccharide is glucose.Monosaccharides contIt has the molecular formula C6H12O6 and the atoms are arranged in a ring.Fructose and Galactose have similar structures.All three of these molecules contain a number of polar OH groups, enabling them to form hydrogen bonds with water.As a results monosaccharides are highly soluble in water.

GlucoseIs the key energy source in most forms of life.It is also a major component of the larger CHOs.Glucose and its polymer, starch, are more rapidly digested than other forms of food. Fructose & GalactoseAre not a abundant as glucose.Galactose is not found in nature as a free monosaccharide.It occurs frequently as a component of larger CHOs.Fructose is found in many fruit juices and honey.Although fructose is a component of other large biological molecules, its main role in the body is an energy source.DisaccharidesIs the carbohydrate formed when two monosaccharides undergo a condensation reaction.They too dissolve in water, taste sweet and are called sugars.Maltose is formed when two glucose molecules react, with the elimination of a water molecule. Notice how the hydroxyl functional groups react to form the dissacharide and water.The two rings are joined via an oxygen atom.This linkage is called a ether (or glycosidic) linkage.

Disaccharides contLactose and Sucrose are two other disaccharides.Lactose is made from a condensation reaction of glucose and galactose.It is not as sweet as glucose.Lactose is synthesised in the mammary glands of mammals and is the main CHO in milk.Sucrose is formed from a condensation reaction of glucose and fructose.It is widely used as a sweetener.It is found in the sap of trees and the juices of many fruits.

PolysaccharidesAre polymer carbohydrates made by linking monosaccharides into a chain.They are polymers of glucose molecules linked together in different ways by condensation reactions.They are generally insoluble in water and have no taste.The three most important polysaccharides are: glycogen, starch and cellulose.GlycogenIs found in animals, where it acts as a glucose storage molecule.As glucose can be oxidised to produce energy more rapidly than fat, all glucose is polymerised to glycogen to be stored.When there is no more storage space for glycogen, the glucose is converted into fat.As energy is required, the glycogen is hydrolysed to yield glucose for respiration.StarchThe glucose storage molecule in plants; the plants equivalent of glycogen.The starch is stored and used at night to meet the plants ongoing energy requirements when the glucose production from photosynthesis has ceased.DigestionDuring digestion, the polymers must be broken down to release the glucose monomers.The polymers are first hydrolysed.This hydrolysis is catalysed by enzymes; every 2nd glucose is hydrolysed to produce maltose.Another enzyme catalyses the hydrolysis of maltose into glucose, which absorbed into the body.These can be regarded as the reverse of condensation reactions.

CelluloseThe main structural material in plants.It has a Mr ranging from 50,000 to 2.5 million.Its chemical structure differs from starch and glycogen because of the difference that the way the glucose monomers are joined.

StarchCellulose

ProteinsProteins are found in every cell and are fundamental to cell structure and operation.There are thousands of different types of proteins and each has its own purpose.

Amino AcidsProteins are polymers built up from monomer molecules called amino acids.Two of the simpler amino acids are glycine and alanine.Every amino acid has an amine group and a carboxyl group.They have the general formula of H2N-CHZ-COOHThe major difference between amino acid is the collection of atoms that make up the side chain, known as the Z group.

Amino Acids

Valine* valThreonine* ThrSerine serTyrosine TyrTryotophan* Trp

Amino Acids contAs a consequence of the polar amino and carboxyl functional groups; amino acids are soluble in water.In solution, the amino group can acts as a base, and the carboxyl as an acid.As a result, the amino acid molecule in a solution at a particular pH will usually be in the form of +H3N-CHZ-COO-.This sort of molecule is called a zwitterion or dipolar ion.ZwitterionA proton has been lost from the acidic carboxyl group and the basic amino group has gained a proton.The pH at which an amino acid exists as a zwitterion depends on the structure of the Z group.The dual acidic and basic nature of amino acids means that several different forms of an amino acid can be in equilibrium in a solution.The predominant form depends on the acidity of the solution.In acidic solutions, the +H3N-CHZ-COOH form is most abundant, whereas H2N-CHZ-COO- form is most abundant in alkaline solutions.Amino Acids contThe ability of amino acids to react with both acids and bases means that they can act as buffers. This means they minimise the effect that the addition of H+ or OH- ions to a solution would have on acidity.Protein StructureWhen a molecule containing a COOH combines with a molecule containing NH2, a condensation reaction occurs to form an amide functional group CONH2-.This links the two molecules.Water is also formed.

Protein Structure contProteins are polymners formed by condensation reactions between amino acids.During these reactions the amino acids join and form long unbranched chains.The amine group of one amino acid reacts with the carboxyl of another.A covalent bond is formed and a molecule of water is eliminated.PeptidesMolecules made from amino acids are often called peptides.When two amino acid molecules react together it is called a dipeptide.When three molecules react and tripeptide is formed.A polymer made from amino acids is known as a polypeptide.Polypeptides built up of more than 50 amino acids are usually called proteins.The group of atoms CONH- that links the amino acids is an amide group, referred to as a peptide linkage in proteins.StructureThe role that any protein fulfils is dependent on its shape. This is regarded as being made up of a primary, secondary and tertiary structure.

Primary StructureThe order of the amino acids is known as the primary structure.The entire shape of a protein is a consequence of the order in which the AAs are joined.

Secondary StructureParts of the chain can attract each other creating 3D shapes.This coiling, folding or pleating of sections is described as the proteins secondary structure.

Tertiary StructureThe Z groups in the amino acid units of a protein influence the overall 3D shape of the molecule.The Z groups in some amino acids are relatively large and their size can cause distortions in the protein structure.Further, some of the side groups are capable of forming bonds with side groups elsewhere on the protein chain.As a consequence of such bonds, a variety of protein shapes exist.The overall 3D shape adopted by the protein is called its tertiary structure.

EnzymesMany chemical reactions occur more rapidly when a catalyst is present.The biological catalysts that accelerate the rate of chemical reactions in living things are a type of protein called enzymes.Enzymes control the manufacture of complex substances as well as breaking down the chemicals to provide energy.Enzymes contThey are usually more efficient than inorganic catalysts, because they allow reactions to occur rapidly within the narrow band of temperature in which life can survive.Compared to inorganic catalysts:Enzymes produce much faster reactions rates: they can increase the rate of a reaction by as much as 1010 times.Enzymes operate under milder conditions.Enzymes are more sensitive: The catalytic activity of many enzymes is destroyed when they are heated strongly because their delicate structure breaks down. The enzyme is then described as being denatured.Enzymes are very selective.Enzymes contThe catalytic activity of an enzyme depends on its tertiary structure.A slight change in its 3D shape can render an enzyme inoperative.The active site of an enzyme is usually a flexible hollow or cavity within the molecule.Some enzymes have small, non-protein parts called cofactors, such as vitamins or metal atoms associated with the active site.These cofactors are necessary for catalytic effect.Thank You